Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,594,256	(C)8→9	pseudogene (3732/3861 nt)	yneO ←	pseudogene, AidA homolog

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,594,248	1	.	C	100.0%	160.4 / NA	44	pseudogene (3740/3861 nt)	yneO	pseudogene, AidA homolog
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (28/16);  total (28/16)

GACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCA  >  NC_000913/1594114‑1594376                                                                                                                                        |                                                                                                                                 gACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑cccc                                                                                                                              >  1:346740/1‑139 (MQ=255)         gcgCCCCCCCCAGGCATAACGTTCTTATCCCCCGCATTGGTGACATTTCCCGAAATCACACCGCGGTTATGGTTACTAATGGGTTGACTCTCCATCTCACTGGCAGGGTCCGACCCAAAAGACATTA‑cccccccccacg                                                                                                                      <  1:666643/137‑5 (MQ=255)           cccccccccAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGat                                                                                                                     <  1:788304/138‑1 (MQ=255)               cccccAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATcc                                                                                                                 >  2:736914/1‑139 (MQ=255)                ccccAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCAAAAGCAATTTCCCCCCCCCACGATATccc                                                                                                                >  2:666643/1‑138 (MQ=255)                        aTAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTAccc                                                                                                        >  2:563979/1‑139 (MQ=255)                                cATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATAcgc                                                                                                >  2:380665/1‑139 (MQ=255)                                        cTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAAt                                                                                        >  1:888947/1‑139 (MQ=255)                                         tGCAGTGGTGACATTTTCCGACATCACACCGCTGGTATGGGTATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATc                                                                                       <  1:736914/139‑1 (MQ=255)                                                     aTTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGt                                                                           <  2:346740/139‑1 (MQ=255)                                                                 cacaCCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGTACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGt                                                               >  1:603846/1‑139 (MQ=255)                                                                   cacCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTAc                                                             <  1:380665/139‑1 (MQ=255)                                                                           ttATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGtttt                                                     >  2:700322/1‑139 (MQ=255)                                                                                     tAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATc                                                                                       >  2:328282/1‑95 (MQ=255)                                                                                     tAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATc                                                                                       <  1:328282/95‑1 (MQ=255)                                                                                     tAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCac                                           >  1:322971/1‑139 (MQ=255)                                                                                          tgtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccg                                         >  1:27268/1‑136 (MQ=255)                                                                                          tgtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccg                                         <  2:27268/136‑1 (MQ=255)                                                                                           gtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCCCATCaccgctac                                     >  1:676115/1‑139 (MQ=255)                                                                                            ttGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTAc                                                             <  2:106345/114‑1 (MQ=255)                                                                                            ttGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTAc                                                             >  1:106345/1‑114 (MQ=255)                                                                                            ttGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctacc                                    >  2:531551/1‑139 (MQ=255)                                                                                            ttGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctacc                                    >  2:381449/1‑139 (MQ=255)                                                                                            ttGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctacc                                    >  1:382212/1‑139 (MQ=255)                                                                                              gACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGatat                                                                                                                   <  1:415153/58‑1 (MQ=255)                                                                                              gACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGatat                                                                                                                   >  2:415153/1‑58 (MQ=255)                                                                                               aCTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctaccgct                                 >  2:538472/1‑139 (MQ=255)                                                                                                  tGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGAt                              >  1:74516/1‑139 (MQ=255)                                                                                                    ccATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGaa                                                                                         <  2:365418/78‑1 (MQ=255)                                                                                                    ccATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGaa                                                                                         >  1:365418/1‑78 (MQ=255)                                                                                                    ccATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑cccccc                                                                                                                            <  1:63937/42‑1 (MQ=255)                                                                                                    ccATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑cccccc                                                                                                                            >  2:63937/1‑42 (MQ=255)                                                                                                             tGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCcgtc                                                                                                              <  1:457993/48‑1 (MQ=255)                                                                                                             tGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCcgtc                                                                                                              >  2:457993/1‑48 (MQ=255)                                                                                                              ggCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATa                                                                                                   >  2:551977/1‑58 (MQ=255)                                                                                                              ggCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATa                                                                                                   <  1:551977/58‑1 (MQ=255)                                                                                                                  gagTCGGAACCGAAAGCAATTTCCCCCCCCCACGat                                                                                                                     >  2:885201/1‑36 (MQ=255)                                                                                                                  gagTCGGAACCGAAAGCAATTTCCCCCCCCCACGat                                                                                                                     <  1:885201/36‑1 (MQ=255)                                                                                                                  gagTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATcc                                                                   >  2:258233/1‑86 (MQ=255)                                                                                                                  gagTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATcc                                                                   <  1:258233/86‑1 (MQ=255)                                                                                                                  gagTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGTTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGcc              >  1:618587/1‑139 (MQ=255)                                                                                                                   agTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCgt                                                                                     <  2:905199/67‑1 (MQ=255)                                                                                                                   agTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGccc             >  2:906574/1‑139 (MQ=255)                                                                                                                   agTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGccc             >  2:579647/1‑139 (MQ=255)                                                                                                                   agTCGGAACCGAAAGCAATTTCCCCCCCCCACGATATCCGCCGTACCCTGATACGCCGCGGAATCgt                                                                                     >  1:905199/1‑67 (MQ=255)                                                                                                                          aCCGAAAGCCATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACg      <  1:538472/139‑1 (MQ=255)                                                                                                                          aCCGAAAGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACg      <  1:700322/139‑1 (MQ=255)                                                                                                                              aaaGCAATTTCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCa  >  2:237455/1‑139 (MQ=255)                                                                                                                                        |                                                                                                                                 GACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCA  >  NC_000913/1594114‑1594376

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑